Variant report

Variant	rs556808656
Chromosome Location	chr1:45672546-45672547
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45671302-45672673	MCF-7	breast:	n/a	n/a
2	HA-E2F1	chr1:45671804-45672826	MCF-7	breast:	n/a	chr1:45672052-45672062 chr1:45672049-45672059 chr1:45672103-45672112 chr1:45672130-45672139 chr1:45672239-45672248
3	POLR2A	chr1:45671601-45672604	Hela-S3	cervix:	n/a	n/a
4	MTA3	chr1:45672410-45672752	GM12878	blood:	n/a	n/a
5	MAX	chr1:45671458-45672574	ECC-1	luminal epithelium:	n/a	chr1:45672091-45672100
6	REST	chr1:45670473-45672843	H1-neurons	neurons:	n/a	n/a
7	TCF7L2	chr1:45671457-45672594	HCT-116	colon:	n/a	n/a
8	TAF1	chr1:45672410-45672665	H1-hESC	embryonic stem cell:	n/a	n/a
9	RCOR1	chr1:45671744-45672802	Hela-S3	cervix:	n/a	n/a
10	MAX	chr1:45671250-45672606	Hela-S3	cervix:	n/a	chr1:45672091-45672100
11	POLR2A	chr1:45671714-45672608	ECC-1	luminal epithelium:	n/a	n/a
12	CHD2	chr1:45672187-45672643	HepG2	liver:	n/a	n/a
13	ZKSCAN1	chr1:45671739-45673236	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr1:45671342-45672807	IMR90	lung:	n/a	n/a
15	MXI1	chr1:45671307-45672673	HepG2	liver:	n/a	n/a
16	MAZ	chr1:45671343-45672629	Hela-S3	cervix:	n/a	chr1:45672091-45672100
17	RFX5	chr1:45671800-45672649	Hela-S3	cervix:	n/a	chr1:45672628-45672641
18	POLR2A	chr1:45671241-45672825	H1-neurons	neurons:	n/a	n/a
19	SIN3A	chr1:45670734-45672798	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:45671347-45672591	MCF-7	breast:	n/a	n/a
21	MXI1	chr1:45671918-45672659	Hela-S3	cervix:	n/a	n/a
22	HA-E2F1	chr1:45671603-45672636	Hela-S3	cervix:	n/a	chr1:45672052-45672062 chr1:45672049-45672059 chr1:45672103-45672112 chr1:45672130-45672139 chr1:45672239-45672248
23	SMC3	chr1:45672300-45673055	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:45671817-45672642	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:45671606-45672830	H1-neurons	neurons:	n/a	n/a
26	MXI1	chr1:45670219-45673038	SK-N-SH	brain:	n/a	n/a
27	YY1	chr1:45671287-45672583	HepG2	liver:	n/a	chr1:45672283-45672297 chr1:45672048-45672062 chr1:45672048-45672057 chr1:45672130-45672139
28	SIN3AK20	chr1:45671228-45672793	PANC-1	pancreas:	n/a	n/a
29	UBTF	chr1:45671229-45672551	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45672524-45672574	RPTEC	kidney:	n/a
2	chr1:45672524-45672574	SK-N-SH_RA	brain:	n/a
3	chr1:45672524-45672574	MCF10A-Er-Src	breast:	n/a
4	chr1:45672524-45672574	PANC-1	pancreas:	n/a
5	chr1:45672524-45672574	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:45672524-45672574	Hepatocyte	liver:	n/a
7	chr1:45672524-45672574	BJ	skin:	n/a
8	chr1:45672524-45672574	NH-A	brain:	n/a
9	chr1:45672524-45672574	ProgFib	skin:	n/a
10	chr1:45672524-45672574	HEK293	kidney:	embryo
11	chr1:45672524-45672574	HRE	kidney:	n/a
12	chr1:45672524-45672574	H1-hESC	embryonic stem cell:	embryo
13	chr1:45672524-45672574	CMK	blood:	n/a
14	chr1:45672524-45672574	NT2-D1	testis:	n/a
15	chr1:45672524-45672574	Caco-2	colon:	n/a
16	chr1:45672524-45672574	GM19239	blood:	n/a
17	chr1:45672524-45672574	HCF	heart:	n/a
18	chr1:45672524-45672574	SKMC	muscle:	n/a
19	chr1:45672524-45672574	AG04449	skin:	fetal
20	chr1:45672524-45672574	NHDF-neo	bronchial:	n/a
21	chr1:45672524-45672574	ECC-1	luminal epithelium:	n/a
22	chr1:45672524-45672574	MCF-7	breast:	n/a
23	chr1:45672524-45672574	HCPEpiC	choroid plexus:	n/a
24	chr1:45672524-45672574	HMEC	breast:	n/a
25	chr1:45672524-45672574	ovcar-3	ovarian:	n/a
26	chr1:45672524-45672574	PrEC	prostate:	n/a
27	chr1:45672524-45672574	AG10803	skin:	n/a
28	chr1:45672524-45672574	SK-N-SH	brain:	n/a
29	chr1:45672524-45672574	HCT-116	colon:	n/a
30	chr1:45672524-45672574	HIPEpiC	eye:	n/a
31	chr1:45672524-45672574	SK-N-MC	brain:	n/a
32	chr1:45672524-45672574	Jurkat	blood:	n/a
33	chr1:45672524-45672574	AG09309	skin:	n/a
34	chr1:45672524-45672574	GM12892	blood:	n/a
35	chr1:45672524-45672574	T-47D	breast:	n/a
36	chr1:45672524-45672574	LNCaP	prostate:	n/a
37	chr1:45672524-45672574	HEEpiC	esophagus:	n/a
38	chr1:45672524-45672574	IMR90	lung:	fetal
39	chr1:45672524-45672574	HRCEpiC	kidney:	n/a
40	chr1:45672524-45672574	SAEC	small airway:	n/a
41	chr1:45672524-45672574	AG04450	lung:	fetal
42	chr1:45672524-45672574	K562	blood:	n/a
43	chr1:45672524-45672574	GM06990	blood:	n/a
44	chr1:45672524-45672574	NHBE	bronchial:	n/a
45	chr1:45672524-45672574	HL-60	blood:	n/a
46	chr1:45672524-45672574	U87	brain:	n/a
47	chr1:45672524-45672574	HepG2	liver:	n/a
48	chr1:45672524-45672574	A549	lung:	n/a
49	chr1:45672524-45672574	NB4	blood:	n/a
50	chr1:45672524-45672574	HRPEpiC	eye:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45480075..45485962-chr1:45670647..45674355,5	MCF-7	breast:
2	chr1:45672068..45672603-chr3:150125909..150126562,2	Hela-S3	cervix:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPDL-1	chr1:45672404-45672689	XLOC_000167
2	lnc-HPDL-1	chr1:45672409-45675890	NONHSAT002922

No data

Variant related genes	Relation type
ZSWIM5	TF binding region
ZSWIM5	CpG island
ENSG00000196428	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	esv3365432	chr1:45670715-45673638	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3444099	chr1:45670790-45673738	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45668000-45673800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:45668600-45672800	Active TSS	Fetal Brain Female	brain
3	chr1:45669400-45673200	Active TSS	Brain Angular Gyrus	brain
4	chr1:45669400-45673400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:45669600-45672600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:45670000-45672600	Active TSS	Brain Anterior Caudate	brain
7	chr1:45670000-45672600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr1:45670000-45672800	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr1:45670000-45673200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:45670000-45673400	Active TSS	Ovary	ovary
11	chr1:45670200-45672600	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:45670200-45672600	Active TSS	Brain Hippocampus Middle	brain
13	chr1:45670200-45672600	Active TSS	Duodenum Mucosa	Duodenum
14	chr1:45670200-45672800	Active TSS	Rectal Smooth Muscle	rectum
15	chr1:45670400-45672600	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:45670400-45672600	Active TSS	Hela-S3	cervix
17	chr1:45670400-45673200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:45670600-45672600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:45670600-45672600	Active TSS	Brain Substantia Nigra	brain
20	chr1:45670600-45672600	Active TSS	Fetal Intestine Small	intestine
21	chr1:45670600-45672600	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:45670600-45672800	Active TSS	NHLF	lung
23	chr1:45670600-45673000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:45670600-45673000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:45670600-45673200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:45670600-45673200	Active TSS	Colonic Mucosa	Colon
27	chr1:45670800-45672600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:45670800-45672600	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:45670800-45672800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:45670800-45672800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:45670800-45672800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr1:45670800-45672800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:45670800-45672800	Active TSS	Fetal Kidney	kidney
34	chr1:45670800-45672800	Bivalent/Poised TSS	HepG2	liver
35	chr1:45670800-45673000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:45670800-45673000	Active TSS	Pancreas	Pancrea
37	chr1:45671000-45672600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:45671000-45672600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:45671000-45672600	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr1:45671000-45672600	Active TSS	Psoas Muscle	Psoas
41	chr1:45671000-45672600	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr1:45671000-45672800	Active TSS	Small Intestine	intestine
43	chr1:45671000-45672800	Bivalent/Poised TSS	Thymus	Thymus
44	chr1:45671000-45673000	Active TSS	Aorta	Aorta
45	chr1:45671000-45673000	Active TSS	Right Ventricle	heart
46	chr1:45671200-45672600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:45671200-45672600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:45671200-45672600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:45671200-45672600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:45671200-45672600	Active TSS	Primary T helper naive cells from peripheral blood	blood

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